Choose the appropriate size drill bit (not too big, not too small). I forget now which size I used, sorry. I suggest doing the passenger side first as there are more unused pins on that side. Also, all my pictures are from the drivers side.

Slide the "lock" up on the body side connector to release the harness.

Pull up the orange slide on the door harness and then press the clips on the sides to release it.

Now you have room to drill both. I cut the zip tie on the door harness and removed that boot to make it easier to work with. I also had to remove the top boot (big pain to work with, beware) to cut a hole to run the wires into the cab.
On the top of the door connector, see pictures, there is a blue wire that is not used (there is no wire on the body side connector). That's where I drilled and ran my wires.

I used a 14gauge solid core wire to pull the wires from the door, through the boot and into the cab.

When re-connecting the harnesses just be sure and keep some tension on the wires so they don't get kinked in there.
Also, after you've got your wires ran and the connectors back together VERIFY THE DOOR HINGE (it moves into the door when closed) DOES NOT CATCH ON ANY WIRES! Mine did and a wire got pinched or broken and I had to fix it after I put it all back together, that sucked.

Cool, I'm thinking of doing this as well wanted to see what was involved. I have some super thin telephone interconnect wire I thought of using but can see that might risk breaking or might not be high enough gauge to handle the switch.

Cool, I'm thinking of doing this as well wanted to see what was involved. I have some super thin telephone interconnect wire I thought of using but can see that might risk breaking or might not be high enough gauge to handle the switch.

I'm not sure what guage wire they used. It's pretty close if not exactly the stock size.

Thanks OmniCamaro! This thread combined with your rudimentary wiring diagram are what I used to complete my install (well, passenger side... still have the driver's side to go).

Oh, may I suggest that you post a link to this thread in the Door lock DIY thread by Dwalex? Someone asked me about the drilling method and I noticed that I wouldn't have found this thread except I did a random Google search.

I found it easier to drill out the area above the connector. Fit wires through no problem. I highly recommend disconnecting the battery b4 doing this. Very long process getting windows working properly again, haha.